This happens when I add Analytics: Y-Axis Constant Line to the stacked column chart using a measure for Value field, but I assume it's relevant to other chart types.
The visual displays 0% line on the bottom of the column despite the measure used for the Value field returns BLANK(). Also having Y-Axis Start greater than 0% doesn't fix the problem. It still shows the 0% line on the bottom of the column, even when axis Y starts from much bigger value (e.g. 75%).